447 Open source projects that are alternatives of or similar to Fgbio

A robust model for quantitative comparison of ChIP-Seq data sets.

A package for designing compact and comprehensive capture probe sets.

Method to optimally select samples for validation and resequencing

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

NGLess: NGS with less work

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

R package for analyzing single-cell RNA-seq data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

(No maintenance) Detect gene fusion directly from raw fastq files

Data intensive science for everyone.

Java utilities for Bioinformatics

C library for high-throughput sequencing data formats

Tools to process and analyze deep sequencing data.

UGENE is free open-source cross-platform bioinformatics software

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Project metadata manager for PEPs in Python

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

A simplified pipeline for ctDNA sequencing data analysis

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Official code repository for GATK versions 4 and up

A tool to circularize genome assemblies

Single cell perturbation prediction

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Next generation sequencing reads de novo assembler.

Application for making ENCODE Blacklists

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

dna2vec: Consistent vector representations of variable-length k-mers

APBS - software for biomolecular electrostatics and solvation

The sources of the openSNP website

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

Bayesian haplotype-based mutation calling

A cool place to store your Hi-C

An efficient FASTQ manipulation suite

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

Bio4j abstract model and general entry point to the project

A comprehensive library for computational molecular biology

Benchmarking programming languages/implementations for common tasks in Bioinformatics

nim wrapper for htslib for parsing genomics data files

Python module for average nucleotide identity analyses

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

RNA-seq workflow using STAR and DESeq2

Bioconductor cheat sheet

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Fast multi-line FASTA/Q reader in several programming languages

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

A Practical and Efficient NCBI Taxonomy Toolkit

Simple simulation of single-cell RNA sequencing data

SortMeRNA: next-generation sequence filtering and alignment tool

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Package for fetching metadata and downloading data from SRA/ENA/GEO

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

A collection of scripts and notes related to genomics and bioinformatics